中国野生种葡萄及种间杂种VvmybA1基因型和表达分析

【目的】检测中国野生种葡萄以及山欧杂交品种VvmybA1基因型,并对不同材料VvmybA1基因序列进行比对分析,通过对山欧杂种VvmybA1的基因型和表达分析,揭示白色杂交品种‘熊岳白葡萄’果皮无花色苷合成的分子机理。【方法】设计特异性引物,在DNA水平上利用分子克隆手段和绝对荧光定量PCR方法,检测葡萄属的不同样品VvmybA1基因型。采用相对荧光定量PCR手段,对山欧杂交品种果实转色过程中VvmybA1和UFGT的表达量进行分析。【结果】①检测的中国野生种葡萄材料不存在VvmybA1a等位基因;②与欧亚种葡萄相比,中国野生葡萄VvmybA1基因在启动子、内含子以及第三个外显子区域存在不同程度碱基的缺失、插入和替换,表现出丰富的遗传多样性。而且许多野生种葡萄VvmybA1基因的内含子、外显子和启动子区域存在一些特有序列或突变,这些位点可筛选作为鉴别葡萄种和品种的分子标记;③在‘公酿1号’、‘北红’、‘熊岳白葡萄’等山欧杂交葡萄品种以及分类地位未定的‘宿晓红’葡萄中检测到VvmybA1a等位基因,并且‘熊岳白葡萄’为VvmybA1a纯合类型;④RT-PCR分析结果表明,在葡萄果皮转色过程中,‘公酿1号’葡萄果皮VvmybA1和UFGT的表达量增加,然而在‘熊岳白葡萄’果实成熟期未检测到VvmybA1和UFGT 的表达。【结论】证明VvmybA1a等位基因是欧亚种葡萄以及其杂交种独有的基因型,不存在于中国野生种葡萄中,推测‘宿晓红’葡萄具有欧亚种葡萄血缘;葡萄属不同种的VvmybA1基因序列比对分析揭示,山欧杂交品种‘熊岳白葡萄’果皮不能合成花色苷是由于VvmybA1a纯合,VvmybA1不表达。     

Population structure of Phytophthora infestans in Turkey reveals expansion and spread of dominant clonal lineages and virulence

Late blight, caused by the oomycete Phytophthora infestans, is considered the most important and destructive disease of potato in Turkey. In this study, characterization of 367 isolates of P. infestans obtained from the potato-growing areas of the country was carried out to evaluate the pathogen population structure over the 2017–2019 production seasons. The isolates were characterized by numerous features including mating type, in vitro mefenoxam sensitivity, simple-sequence repeat (SSR) markers, and virulence against a set of potato differential lines. Most isolates were A2 mating type (353 isolates). Also, 68% of isolates were resistant to mefenoxam; the remainder were intermediate in their sensitivity and there were no sensitive isolates. SSR-based genotypic analysis of P. infestans populations showed a low genetic diversity. The 13_A2 clonal lineage predominated with a frequency of 92.1%, followed by 34_A1 (3.3%) and 37_A2 (2.7%). Genotypes 34_A1 and 37_A2 were detected only in 2019. This is the first report of 34_A1 and 37_A2 clonal lineages causing late blight disease of potato in Turkey. The most abundant virulence type was one overcoming resistance genes R1, R2, R3, R4, R6, R7, R10, and R11. These results emphasized that the migration of individuals and the asexual generation of subclonal differences were the main factors driving the population structure of P. infestans in Turkey.     

基于Maize6H-60K芯片精准分型的玉米DH群体遗传规律研究

为解析玉米双单倍体（doubled haploid,DH）群体的遗传规律,使用自主研发的精准分型策略对‘先玉335’DH群体的Maize6H-60K芯片结果进行筛选校正和解析。结果表明：1）通过剔除单态、杂合、缺失标记,使用精准分型策略对标记准确聚类,获得的18 947个SNPs标记覆盖玉米全基因组。2）该群体在10条染色体上平均交换次数为1.84～1.03次,在6号染色体随体区域的交换次数显著减少。3）该群体在1、2、3、8号染色体上存在明显的偏分离现象;通过高频次、高密度的交换,染色体两臂端粒区域理论分离系数表现出回归到50%的趋势。利用获得的重组交换及分离规律可提高从DH群体中筛选到预期育种材料的准确性。     

Distribution and Genotypic Characterization of Campylobacter jejuni Isolated from Poultry in Split and Dalmatia County,Croatia

Consumption of poultry contaminated with Campylobacter jejuni has been recognized worldwide as the leading cause of campylobacteriosis. Therefore, the aim of our study was to investigate the prevalence and genotype diversity of Campylobacter jejuni in poultry meat intended for consumption in Split and Dalmatia County, which is the second biggest County in Croatia. Furthermore, we also wanted to discover possibly stable clones of C. jejuni appearing in different samples and periods of time, which would indicate their ability to persist in or adapt to poultry. In the period from March 2008 until June 2010, 834 samples of poultry from various sources were examined using a surface swab technique. Isolation of C. jejuni was performed by Preston broth and Karmali agar. Identification of the isolates was carried out using biochemical tests. C. jejuni was found in 84 of 574 chicken samples (14.6%) and in nine of 260 samples of turkey (3.5%). Pulse‐field gel electrophoresis (PFGE) was used to analyse 61 obtained isolates using SmaI and KpnI. Of 22 different macrorestriction profiles (MRP) that were found, five were detected in poultry from both different locations and periods of time. Samples from 11 locations were found to be contaminated with more than two different genotypes of C. jejuni. Interestingly, the same MRP were found both in poultry declared to be of domestic origin and in the poultry imported from abroad. The prevalence of C. jejuni in poultry samples was in accordance with previously reported results. Genotypic analysis indicated that the population of C. jejuni in Split and Dalmatia County was diverse and that multiple strains of C. jejuni could be found in the same poultry samples. Furthermore, the same genotypes were identified from the samples obtained from different locations and periods of time, which could support the theory of a global existence of certain MRP that are able to persist in or adapt to poultry.     

绵羊FSTL3基因g.40674542C>T位点多态性与产羔数的关联分析

文章旨在探究绵羊FSTL3基因g.40674542C>T位点多态性与绵羊产羔数之间的关系,以期为绵羊高繁殖力分子育种提供新的遗传标记。利用全基因组重测序结合Sequenom MassARRAY~SNP技术对常年发情绵羊品种(小尾寒羊、策勒黑羊和湖羊)和季节性发情绵羊品种(滩羊、苏尼特羊和草原型藏羊)FSTL3基因g.40674542C>T位点多态性进行了检测,并与小尾寒羊产羔数进行了关联分析。结果表明:FSTL3基因g.40674542C>T位点存在CC、TC和TT三种基因型,基因型频率和等位基因频率在两种发情模式绵羊品种间差异均不显著(P>0.05);g.40674542C>T位点在6个绵羊品种中均表现为低度多态(PIC<0.25),经卡方适合性检验,该位点在小尾寒羊、湖羊和草原型藏羊中处于哈代温伯格平衡状态(P>0.05),在其余3个绵羊品种中处于哈代温伯格不平衡状态;g.40674542C>T位点不同基因型与小尾寒羊第一、第二以及第三胎产羔数均无显著关联(P>0.05)。说明FSTL3基因g.40674542C>T位点不适合用于小尾寒羊产羔数选育。     

Analysis of Ribosome Genotyping and Antimicrobial Resistance in Enterococcus faecalis Isolated from Pigs and Chickens

This study was to investigate the ribosome genotyping and antimicrobial resistance in Enterococcus faecalis strains isolated from 2 large-scale farms in Shanghai.40 isolates were evaluated for their sensitivity to 12 antimicrobial agents by broth microdilution,and the ribosome genotyping (ribotype) was characterized by the Riboprinter^® Microbial Characterization System.The resistance rates of most antimicrobial drug were relatively high and multidrug resistant strains were detected with more than 80%.4 strains of Enterococcus faecalis isolated from pigs were resistant to vancomycin,including 2 strains of vancomycin highly resistant (MIC>64 mg/L) with the same time highly resistant to gentamicin and streptomycin (MIC>2 048 mg/L).The results showed that multidrug resistance of Enterococcus faecalis was a serious issue,and the resistant phenotypes of the same type of ribotype was not entirely consistent.     

PFGE Genotyping and Serotype Analysis of Salmonella Isolated from Goose,Anserindicus and Cygnus

To understand the Salmonella epidemic characteristics and pulsed field gel electrophoresis（PFGE）genotyping of goose,Anserindicus and Cygnus,33 strains of Salmonella were serotype typed by PFGE and genotyped with BioNumerics 6.6 cluster analysis software.The results showed that there were 16 PFGE patterns,which displayed 6 strains Salmonella paratyphi C,19 strains Salmonella thompson,1 strains Salmonella paratyphi B,1 strain Salmonella irumu,1 strain Salmonella oslo,5 undifferentiated.PFGE similarity is about 53.7% to 100.0%,and most of the strains and anthropogenic strains similarity was more than 80%.The results showed that goose,Anserindicus and Cygnus Salmonella serotypes same PFGE type with a high degree of similarity,and possibly from the same clone,quite different serotypes PFGE band pattern difference.     

Bias in heritability estimates from genomic restricted maximum likelihood methods under different genotyping strategies

We investigated the effects of different strategies for genotyping populations on variance components and heritabilities estimated with an animal model under restricted maximum likelihood (REML), genomic REML (GREML), and single‐step GREML (ssGREML). A population with 10 generations was simulated. Animals from the last one, two or three generations were genotyped with 45,116 SNP evenly distributed on 27 chromosomes. Animals to be genotyped were chosen randomly or based on EBV. Each scenario was replicated five times. A single trait was simulated with three heritability levels (low, moderate, high). Phenotypes were simulated for only females to mimic dairy sheep and also for both sexes to mimic meat sheep. Variance component estimates from genomic data and phenotypes for one or two generations were more biased than from three generations. Estimates in the scenario without selection were the most accurate across heritability levels and methods. When selection was present in the simulations, the best option was to use genotypes of randomly selected animals. For selective genotyping, heritabilities from GREML were more biased compared to those estimated by ssGREML, because ssGREML was less affected by selective or limited genotyping.     

Accounting for population structure in selective cow genotyping strategies

The objective of the present study was to investigate the impact of considering population structure in cow genotyping strategies over the accuracy and bias of genomic predictions. A small dairy cattle population was simulated to address these objectives. Based on four main traditional designs (random, top‐yield, extreme‐yield and top‐accuracy cows), different numbers (1,000; 2,000 and 5,000) of cows were sampled and included in the reference population. Traditional designs were replicated considering or not population structure and compared among and with a reference population containing only bulls. The inclusion of cows increased accuracy in all scenarios compared with using only bulls. Scenarios accounting for population structure when choosing cows to the reference population slightly outperformed their traditional versions by yielding higher accuracy and lower bias in genomic predictions. Building a cow‐based reference population from groups of related individuals considering the frequency of individuals from those same groups in the validation population yielded promising results with applications on selection for expensive‐ or difficult‐to‐measure traits. Methods here presented may be easily implemented in both new or already established breeding programs, as they improved prediction and reduced bias in genomic evaluations while demanding no additional costs.     

鲁中肉羊BMP4基因g.63454744 T>G位点多态性与产羔数的关联分析

为了探索骨形态发生蛋白4(Bone morphogenetic protein 4,BMP4)基因g.63454744T>G位点多态性与绵羊产羔数之间的关系,对前期重测序中筛选得到的BMP4基因编码区错义突变单核苷酸多态性位点(Single nucleotide polymorphism site, SNP)g.63454744T>G在384只鲁中肉羊中利用Sequenom MassARRAY~? SNP技术进行分型,再将分型结果与鲁中肉羊产羔数进行关联分析。结果表明:BMP4基因g.63454744T>G位点在鲁中肉羊中存在TT、GT和GG三种基因型;该位点在鲁中肉羊中表现为中度多态(0.250.05)。说明BMP4基因g.63454744T>G位点不适合用于鲁中肉羊产羔数选育。